Bio::Tools::Run::Phylo::Hyphy::Modeltest - Wrapper around the Hyphy Modeltest
analysis
use Bio::Tools::Run::Phylo::Hyphy::Modeltest;
use Bio::AlignIO;
use Bio::TreeIO;
my $alignio = Bio::AlignIO->new(-format => 'fasta',
-file => 't/data/hyphy1.fasta');
my $aln = $alignio->next_aln;
my $treeio = Bio::TreeIO->new(
-format => 'newick', -file => 't/data/hyphy1.tree');
my $modeltest = Bio::Tools::Run::Phylo::Hyphy::Modeltest->new();
$modeltest->alignment($aln);
$modeltest->tree($tree);
my ($rc,$results) = $modeltest->run();
This is a wrapper around the Modeltest analysis of HyPhy ([Hy]pothesis Testing
Using [Phy]logenies) package of Sergei Kosakowsky Pond, Spencer V. Muse, Simon
D.W. Frost and Art Poon. See http://www.hyphy.org for more information.
This module will generate the correct list of options for interfacing with
TemplateBatchFiles/Modeltest.bf.
User feedback is an integral part of the evolution of this and other Bioperl
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The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Valid and default values for Modeltest are listed below. The default values are
always the first one listed. These descriptions are essentially lifted from
the python wrapper or provided by the author.
Title : valid_values
Usage : $factory->valid_values()
Function: returns the possible parameters
Returns: an array holding all possible parameters. The default
values are always the first one listed. These descriptions are
essentially lifted from the python wrapper or provided by the author.
Args : None
Title : new
Usage : my $obj = Bio::Tools::Run::Phylo::Hyphy::Modeltest->new();
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::Modeltest object
Returns : Bio::Tools::Run::Phylo::Hyphy::Modeltest
Args : -alignment => the Bio::Align::AlignI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-tree => the Bio::Tree::TreeI object
-params => a hashref of parameters (all passed to set_parameter)
-executable => where the hyphy executable resides
See also: Bio::Tree::TreeI, Bio::Align::AlignI
Title : run
Usage : my ($rc,$results) = $modeltest->run($aln);
Function: run the modeltest analysis using the default or updated parameters
the alignment parameter must have been set
Returns : Return code, hash containing the "Hierarchical Testing" and "AIC" results, both as hashes.
Args : L<Bio::Align::AlignI> object,
L<Bio::Tree::TreeI> object [optional]
Title : create_wrapper
Usage : $self->create_wrapper
Function: It will create the wrapper file that interfaces with the analysis bf file
Example :
Returns :
Args :